This Web page contains the URLs and annotations for the Web-accessible resources listed in Guide to Reference and Information Sources in Plant Biology, published by Libraries Unlimited in December 2005.
Chapter 8. Genetics, Molecular Biology, and Biotechnology
The University of Texas at Austin's Biotech Resources Web Project provides this freely accessible dictionary, originally developed at the Indiana Institute for Molecular and Cellular Biology, of more than 8,300 life science terms. The focus is biochemistry, biotechnology, botany, cell biology, and genetics. Site has not been recently updated but is cited by many.
Funded by the National Science Foundation (NSF), this group aims to develop controlled vocabularies (ontologies) that describe plant structures and developmental stages, providing a semantic framework for meaningful cross-species queries across genomic databases. All of the major plant database resources are members or collaborators in this endeavor, including the Gramene database, the Arabidopsis Information Resource (TAIR), and the MaizeGDB. The Missouri Botanical Garden, the Open Biological Ontologies project (OBO), the Gene Ontology Consortium (GO), and the Deep Gene project are also collaborators.
ATTC: The Global Bioresource Center. Manassas, VA: American Type Culture Collection (ATTC).
The American Type Culture Collection (ATCC) is a nonprofit, private organization that was established in 1925 to acquire, preserve, and distribute well-characterized biological cultures for the international research community. Culture types that would be of interest to plant biologists include algae, filamentous fungi, yeast, plant tissue cultures, plant seeds, algae, and plant viruses. Presently seventy-five plant cell cultures and over 400 strains of patented seeds are available.
This Web site makes available crop genome databases on Arabidopsis thaliana, barley, Brassica species, forage grasses, millet, tef, and nearly 200 U. K. crop species from British research institutions. Databases on sequenced plant gene nomenclature, plant uses, cereal pathogens, plant ESTs (expressed sequence tags), STSs (sequence tagged sites), and plant gene families are also hosted here. Analysis software is also available for download.
Brendel, Volker and Carol Lushbough. PlantGDB: Resources for Plant Comparative Genomics.
PlantGDB is the home page for the NSF-funded project "PlantGDB - Plant Genome Database and Analysis Tools". Through the development and implementation of integrated databases and analytical tools, the goal of this project and Web site is to aid in the organization and interpretation of plant genome sequence data from three major sources: whole genome sequencing and assembly, genome survey sequencing, and expressed sequence tags (ESTs). The project also includes the development of the BioExtract Server prototype, which provides a distribution point for plant genome data stored in different local and external databases. The Plant Genome Research Outreach Portal (PGROP) was also set up to provide a centralized repository of various NSF-sponsored Plant Genome Research "outreach" programs and activities for the public at large, undergraduates, high-school students and teachers. PGROP seeks to broaden participation of these user groups in plant genome research topics by making information on appropriate programs, materials, and guidance available.
Carnegie Institution of Washington, Dept. of Plant Biology, and National Center for Genome Resources. TAIR, the Arabidopsis Information Resource.
TAIR contains a comprehensive collection of information for the scientific community about the most widely used model flowering plant, Arabidopsis thaliana, which was the first plant sequenced, in 2000. TAIR consists of a searchable relational database that includes many different datatypes such as DNA sequences, genes, proteins, vectors, genetic markers, and citations to publications. It is in the process of transitioning from a genome-centric resource to one that focuses on all aspects of Arabidopsis biology. In July 2002, TAIR logged over 500,000 Web pages visits, making it the most widely used plant biology information resource worldwide.
Entrez: The Life Sciences Search Engine. Bethesda, MD: National Center for Biotechnology Information, 1996- .
Newly redefined, Entrez provides an integrated search engine for nucleotide and protein sequence data from over 100,000 organisms, including thousands of plant species. Additionally Entrez searches 3D protein structures, genomic mapping information, PubMed (MEDLINE) citations, and more. Entrez can be searched with a wide variety of text terms such as author name, journal name, gene or protein name, organism, and other terms, depending on the database being searched. Although certainly not primarily a botanical resource, since plant sequence data are deposited in GenBank (see below) and other nucleotide databases, Entrez provides a valuable tool for accessing plant molecular biology resources and citations. For example, at the time of writing (2004), searching Entrez for the term Arabidopis brought up over 10,000 citations in PubMed, nearly a million nucleotide sequences, over 130,000 protein sequences and over 260,000 GEO gene expression profiles. Formerly the Entrez Browser.
GenBank. Bethesda, MD: National Center for Biotechnology Information.
GenBank is the major gene sequence database. It includes both animal and plant sequences, and may be searched for no fee. GenBank is searchable from the Entrez Nucleotide search engine, where one simultaneously searches nucleotides deposited in GenBank, EMBL (European Molecular Biology Laboratory), DDBJ (DNA Data Bank of Japan), RefSeq (NCBI Reference Sequence), PIR (Protein Information Resource), PRF (Protein Research Foundation), Swiss-Prot Protein knowledgebase, and PDB (RCSB Protein Data Bank). Refer to the citation for Entrez, above, for additional details.
Molecular Biology Database Collection, published as a yearly special issue of Nucleic Acids Research.
Each year since 1991, NAR has devoted one issue to a review and listing of the key databases of value to the biologists interested in various aspects of molecular biology, biochemistry, and genetics. To be included, the database must be freely available to the public, as is the Molecular Biology Database Collection, itself. The 2004 issue (Volume 32, Database Issue) included the URLs and a brief description for 548 databases. Additionally there were over a hundred articles detailing new or updated information for specific databases, at least ten of which were devoted to plants. Online database issues are freely available at http://nar.oupjournals.org. For the past few years, the Database Issue has been the first issue of the year.
Nature Biotechnology Directory. London: Nature Publishing Group, 2003- . Annual. $315.00. ISBN 140392046X (paper).
Deals with the state of biotechnology worldwide. The directory is divided into three parts: profiles of commercial biotechnology companies, universities, institutes, and research organizations; a buyers guide to over 16,000 products, equipment, and services; and contact information for government departments, trade or industry associations, details of available academic grants, and a translation guide to common biotech terms in French, German and English. This comprehensive directory is exceptionally useful, and recommended for a wide group of users and libraries. The directory is searchable and free online.
PlaNet is a distributed, shared effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated plant genome database for the systematic exploration of Arabidopsis and other plants. Current partners include bioinformatics and biotechnology groups from Germany, France, Belgium, The Netherlands, Great Britain, and Spain.
Plant Genomes Central: Genome Projects in Progress. Bethesda, MD: National Center for Biotechnology Information, 2003.
Provides a graphical representation of chromosomes from a variety of plant genomes that can be viewed in their entirety or explored in progressively greater detail, with links to associated sequence data. Additionally, the site features a multi-plant species genome search engine, a plant-customized BLAST search engine for determining similarities, links for species-specific project centers, resources for plant mitochondria and plastid genomes, and links for research centers specializing in plant genome sequencing and analysis.
Sambrook, Joseph and David W. Russell. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2001. 3 vol. $249.00 (set, paper). ISBN 0879695773 (set, paper).
Although not focused on plants, this highly regarded set includes techniques for a wide variety of molecular cloning methods, with their advantages and disadvantages. The appendices are also valuable and include information on media, the preparation of reagents and buffers, properties of nucleic acids, and more. There are extensive references and numerous diagrams. Access to a supporting Web site is provided to purchasers of the set.
Stein, Lincoln, et al. Gramene: A Resource for Comparative Grass Genomics.
Gramene is a relational database built on the genome sequence for rice that allows comparative genome exploration in grasses such as maize, barley, oat, wheat, sorghum, wild rice, and rice. The Gramene database provides information about genetic maps, sequence, genes, genetic markers, mutants, QTLs (quantitative trait loci), controlled vocabularies, and publications.
Germplasm Resources Information Network; National Germplasm Resources Laboratory (U.S.). National Plant Germplasm System. Beltsville, MD: National Germplasm Resources Laboratory, Database Management Unit, 1996.
The National Plant Germplasm System (NPGS) holds the germplasms of grains, vegetables, fruits, ornamentals, and woody landscape plants. The NPGS Web site lists the repositories and their holdings, and provides a request form for specimens for research. GRIN (Germplasm Resources Information Network), a database of stored cultivars, plant variety protection submissions, and crop registration, is available for searching.
Gribskov M. PlantsT: Functional Genomics of Plant Transporters.
PlantsT, funded by the National Science Foundation (NSF), strives to pull together the most current information necessary for researchers to conduct experiments on membrane transport proteins and genes. PlantsT allows researchers to submit their own annotated research discoveries to the site and then propagates this information onto databases such as GenBank (see Handbooks, above), PIR (Protein Information Resource), or Swiss-Prot. Users can search by name or accession number to retrieve plant transporter gene data including protein sequences, annotation information, a transmembrane domain prediction graph, and related protein sequences. Other resources available include outreach program information, movies, genechip tools, and membrane protein family lists, sequence alignments, and phylogenetic trees.
Interagency Working Group on Plant Genomes. Committee on Science. National Science and Technology Council. National Plant Genome Initiative: 2003-2008. Washington: National Science and Technology Council, 2003. 26 p.
The National Plant Genome Initiative (NPGI) was established in 1998 as a coordinated national plant genome research program by the Interagency Working Group (IWG) on Plant Genomes with representatives from the Department of Agriculture (USDA), Department of Energy (DOE), National Institutes of Health (NIH), National Science Foundation (NSF), Office of Science and Technology Policy (OSTP), and the Office of Management and Budget (OMB). In this report, the IWG describes the NPGI plan for the next five years (2003-2008). See also The National Plant Genome Initiative Objectives for 2003-2008, below.
Lineberger, R. Daniel. Plant Tissue Culture Information Exchange.
The Plant Tissue Culture Information Exchange was established by Professor Dan Lineberger of the Department of Horticultural Sciences, Texas A&M University, as part of Aggie Horticulture. The site aims to provide researchers, teachers, and producers worldwide with rapid access to information about plant tissue culture. Resources are organized into sections: micropropagation, which is the most developed section of the Web site, chimeras, protoplasts, embryogenesis, and biotechnology.
The National Plant Genome Initiative Objectives for 2003-2008. Washington DC: National Academies Press, 2002. 75 p. $18.00. ISBN 0309085217.
The National Plant Genome Initiative (NPGI) was launched in 1998 as a long-term project to explore DNA structure and function in plants so that their useful properties could be understood and harnessed to address needs in agriculture, nutrition, energy and waste reduction. For this report, U. S. plant biology experts were asked to make recommendations for the next five-year phase of the Initiative. Among their recommendations: to focus the NPGI portfolio on a small number of key plant species for in-depth development of genome-sequence data and development of functional-genomics tools, translate the basic findings into relevant crop species, use genomics tools to probe for evolutionary relationships, expand bioinformatics tools, and create postdoctoral training opportunities.
The Plant Variety Protection Office (PVPO) administers the Plant Variety Protection Act (PVPA) by issuing Certificates of Protection in a timely manner. The Act provides legal intellectual property rights protection to developers of new varieties of plants which are sexually reproduced (by seed) or tuber-propagated.” The PVPO Web site provides information on the kinds of plants that are eligible for protection, what is protected, exemptions, how to apply, and costs. This site also supplies printable application forms, federal regulations, and links to public databases of protected plant varieties. There are also links to other plant intellectual property organizations and seed industry organizations.
Quatrano, Ralph. Plant Genomics: Emerging Tools. Rockville, MD: American Society of Plant Biologists, 2001. 319 p. $25.00. ISBN 0943088429.
This collection of articles from the journal Plant Cell succinctly pulls together key or review articles on the topics of functional and comparative genomics.
Slater, Adrian, Nigel W. Scott, and Mark R. Fowler. Plant Biotechnology: The Genetic Manipulation of Plants. New York: Oxford University Press, 2003. 346 p. $49.50 (paper). ISBN 0199254680 (paper).
The aim of this textbook, written by members of the Norman Borlaug Institute for Plant Science Research in Leicester, is to provide the reader with a sound knowledge of plant biotechnology. A third of the book is devoted to explaining the underlying science (the organization of genomes, plant tissue culture, plant transformation techniques), with the rest of the book providing a balanced view of the issues involved in producing genetically modified plants including the economic, social, moral and ethical considerations that surround the subject. At the companion Web site, text and illustrations can be downloaded.
Somerville, Chris and Elliot Meyerowitz, eds. The Arabidopsis Book (TAB). Rockville MD: American Society of Plant Biologists, 2002- . ISSN 1543-8120.
The Arabidopsis Book is an Open Access project that is creating an encyclopedic work on one of the most heavily studied model plant species, Arabidopsis thaliana, the first plant fully sequenced. Currently with forty-seven chapters, the book will eventually have over 100 invited chapters reviewing Arabidopsis cellular processes, development, genetics, environmental influences, metabolism and regulatory processes. The chapter authors are committed to frequently update the materials, by themselves or others. With copious references and hyperlinks, TAB is a pioneer in what scholarly resources can be. BioOne freely provides both HTML and PDF versions of each chapter and has implemented a search interface.
Publishes Plant Cell, the most prestigious journal devoted to plant molecular biology studies.
Donald Danforth Plant Science Center. 975 North Warson Road, St. Louis, Missouri 63132. Phone: 314-587-1000.
Founded in 1998, the Donald Danforth Plant Science Center is a not-for-profit plant research institute composed of fourteen laboratories with a mission to improve the human condition by enhancing the nutritional content of plants or to explore novel uses of plants. Current research areas include computational and structural biology, biochemistry, phytochemistry, physiology, genetics, cell biology, and root biology. Sponsors a weekly seminar series as well as an annual symposium.
European Plant Science Organization (EPSO). Technologiepark 927, B-9052 Gent, Belgium. Phone: 32 93 313 810. Fax: 32 93 313 811. E-mail: email@example.com.
EPSO is an independent body that represents fifty-four research institutions from twenty-three European countries. The group was set up in 2000 and its top priorities include facilitating an understanding of modern plant molecular biology, boosting funding for basic plant science and coordinating research activities on national, E. U. levels and beyond. It sponsors a biennial, five-day conference.
Genetics Society of America. 9650 Rockville Pike, Bethesda, MD 20814-3998. Phone: 301-634-7300. Fax: 301-634-7079. E-mail: Elaine Strass, Executive Director, firstname.lastname@example.org.
Founded in 1931, the Genetics Society of America includes over 4,000 scientists and educators interested in the field of genetics. The Society publishes the journal Genetics, and sponsors scientific meetings focused on key organisms widely used in genetic research, including a fungal conference.
Institute of Plant Sciences. Federal Institute of Technology LFW, Universitätsstrasse 2, CH-8092 Zürich, Switzerland. Phone: 41 0 1 632 11 11. Fax: 41 0 1 632 10 37.
Established in 1986, this Swiss institute integrates basic research in the physiology, biochemistry and development of plants, and gene technology with modern agricultural concerns in the areas of plant biology, crop science, and phytomedicine. There are currently over 200 research and support staff at the Institute.
International Association for Plant Tissue Culture and Biotechnology. c/o Professor Zhi-hong Xu, President, Office of the President, Peking University, Beijing 100871 China. Phone: 86 10 6275 1200. Fax: 86 10 6275 1207. E-mail: email@example.com.
The primary activities of the Association have been to organize quadrennial congresses of plant tissue culture and biotechnology, and to publish a newsletter for its membership. Its news is reported as part of the In Vitro Report, published by the Society for In Vitro Biology. Formerly International Council for Plant Tissue Culture.
International Plant Genetics Resources Institute (IPGRI). IPGRI Headquarters, Via dei Tre Denari 472/a, 00057 MACCARESE (Fiumicino), Italy. Phone: 39 06 6118.1. Fax: 39 06 61979661. E-mail: firstname.lastname@example.org.
IPGRI is an international research institute that focuses on the conservation and use of genetic resources important to developing countries. Publications: Geneflow, Descriptors for…, which are publications that proscribe how information about varieties should be gathered. It is a Centre of the Consultative Group on International Agricultural Research (CGIAR) and was founded in 1974 as the International Board for Plant Genetic Resources (IBPGR).
International Society for Plant Molecular Biology (ISPMB). University of Georgia, Biochemistry Department, Athens, GA 30602-7229. Phone: 706-542-3239. Fax: 706-542-2090. E-mail: email@example.com.
Founded in 1982, ISPMB has about 1,850 members. Publishes: Plant Molecular Biology Reporter and is affiliated with Plant Molecular Biology. Sponsors a triennial international congress.
John Innes Centre. Norwich Research Park, Colney, Norwich, NR4 7UH,U.K. Telephone: 44 0 1603 450000. FAX: 44 0 1603 450045. E-mail: firstname.lastname@example.org.
The John Innes Centre, located on the Norwich Research Park (UK), is an international center for research in plant and microbial science. There are about 900 staff at the Centre, including over 150 Ph.D. level research scientists. The scientific research at the Centre makes use of a wide range of disciplines in the biological and chemical sciences, including cell biology, biochemistry, chemistry, genetics and molecular biology, understanding and exploitation of plants and microbes, with special emphasis on yield and productivity, quality and valuable products and environmental interactions.
Max Planck Institute of Molecular Plant Physiology (Max-Planck-Institut für Molekulare Pflanzenphysiologie). Am Mühlenberg 1, 14476 Potsdam-Golm, Germany. Phone: +49 (331) 567 80. Fax: +49 (331) 567 8408. E-mail: email@example.com.
Established in 1992 as one of eighteen new Max Planck institutes created since German reunification, this institute composed of over 250 researchers, staff and students, studies the dynamics of plant metabolism and physiology in the context of the plant system as a whole
Established in 1965 on the campus of Michigan State University with the objective of bringing together a group of experimental plant biologists to work cooperatively on long-term, multi-disciplinary plant research problems. To provide stable research funding, the U.S. Department of Energy (DOE) provides a substantial amount of financial support to the PRL on a continuing basis. There are currently eleven faculty and over eighty research staff and students affiliated with the Lab.
Society for In Vitro Biology. 13000-F York Road, #304, Charlotte, NC 28278. Phone: 704-588-1923 or 888-588-1923. Fax: 704-588-5193. E-mail: firstname.lastname@example.org.
The mission of the Society for In Vitro Biology is to foster the exchange of knowledge of the in vitro biology of cells, tissues, and organs from both plants and animals (including humans), though the focus is decidedly in favor of non-plant culture. In addition to the usual organization information and online bookstore, the home page of the Society includes a library of films and videos that may be rented.
TIGR: The Institute for Genomic Research. Rockville MD, 1999. URL: http://www.tigr.org/
Founded in 1992, The Institute for Genomic Research (TIGR) is a non-profit research institute whose primary research interests are in structural, functional, and comparative analysis of genomes and gene products from a wide variety of organisms including plants. Currently they have the primary Arabidopsis thaliana database, which provides access to genomic sequence data and annotations generated at TIGR and assemblies of Arabidopsis ESTs (expressed sequence tags) from worldwide sequencing projects. TIGR also has sequence and other databases for rice, potato, maize, loblolly pine, and Medicago truncatula (the model legume). Additionally, TIGR houses the Plant Repeat database. Besides the databases, TIGR also provides lists of publicly accessible microarray resources, free gene analysis software tools, protocols, and much more.
Chapter References: National Science Foundation. 2000. “Nifty 50.”
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